3MEK | pdb_00003mek

Crystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with S-adenosyl-L-methionine

PDB DOI: https://doi.org/10.2210/pdb3MEK/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-31 Released: 2010-04-14
Deposition Author(s): Lam, R., Dombrovski, L., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Wu, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.208 (Depositor), 0.208 (DCC)
R-Value Work:
0.174 (Depositor), 0.176 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with S-adenosyl-L-methionine

Lam, R., Dombrovski, L., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Wu, H.

To be published.

Macromolecule Content

Total Structure Weight: 50.58 kDa
Atom Count: 3,559
Modeled Residue Count: 423
Deposited Residue Count: 429
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SET and MYND domain-containing protein 3	A	429	Homo sapiens	Mutation(s): 0 Gene Names: SMYD3, ZMYND1, ZNFN3A1 EC: 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7B4 (Homo sapiens) Explore Q9H7B4 Go to UniProtKB: Q9H7B4
PHAROS: Q9H7B4 GTEx: ENSG00000185420
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H7B4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.208 (Depositor), 0.208 (DCC)
R-Value Work: 0.174 (Depositor), 0.176 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.809	α = 90
b = 65.923	β = 90
c = 108.102	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-04-14

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-04-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary